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The Obama administration acknowledged Tuesday that it missed warnings in the background check of the Washington Navy Yard shooter and promised major changes, including cutting the number of people granted secret clearance and testing whether background investigators should scour applicants’ social media profiles for red flags.

Officials also said they may withhold grant money from police departments that refuse to cooperate with background investigators, after it was revealed that Seattle police never turned over records relating to Aaron Alexis, the Navy Yard shooter, during his background clearance investigation.

In September, Alexis used his secret clearance to gain access to the Navy Yard, where he went on a rampage that left 12 people dead and numerous others wounded before Alexis himself was killed by police.

“I think we all understand that open and free societies are always vulnerable. But together, we’re going to do everything possible to provide our people as safe and secure a workplace as possible,” Defense Secretary Chuck Hagel said as he highlighted steps the Pentagon is taking to try to prevent a repeat of Alexis‘ situation.

The Pentagon promised to try to cut 10 percent of the 2.5 million clearances it has approved. Officials also said they will create a threat management system that will automatically check databases to see whether those who have clearance have had any recent run-ins with the law.

Critics said the reviews focused on structural problems without getting at the fundamental issue that nobody took responsibility for Alexis‘ apparent mental health problems.

“The Department of Veterans Affairs, the United States Navy and local law enforcement officials were in contact with this individual and saw that he was presenting symptoms of a severe mental illness, yet was never referred to psychiatric medical services,” said Rep. Tim Murphy, Pennsylvania Republican. “Everyone who came in contact with him understood there was a problem, but no one acted.”

The background-check system has come under scrutiny after the Navy Yard shooting and after Edward Snowden, a former government contractor, absconded with documents exposing some of the U.S. intelligence community’s secret snooping programs. Both men had been approved for high-level clearances.

In several reports Tuesday, top government officials acknowledged a number of holes in the system.

In one report, officials said agencies don’t have a standard way of dealing with lying in clearance reviews or a policy on suspending clearance when either criminal or mental health red flags are raised.

The reports said the background check on Alexis was conducted by the book yet failed to detect that he was giving them false information. If that had been detected, the review said, it might have led to a denial of clearance.

Officials also said the investigation of Alexis either missed or didn’t get full details on several of his run-ins with the law, including one accusation that he shot out the tires of a construction worker’s car.

House Oversight and Government Reform Committee investigators, who also have looked into the matter, said the problem was that police in Seattle had a policy of refusing full cooperation with background check requests for information. That meant investigators knew of the incident but were not given the full details, including that Alexis had fired a gun.

Seattle has since changed its policy, but the oversight committee said hundreds of other police departments across the country, including in New York, Los Angeles and Baltimore, still don’t fully cooperate.

The Obama administration on Tuesday said it would leverage federal grant money to force state and local police to comply.

Rep. Darrell E. Issa, California Republican and oversight committee chairman, said the administration’s review agrees with his own findings: “Continuous evaluation must be implemented; more data is needed for investigations to be complete, including utilizing social media and other Internet sources; and local law enforcement agencies must comply with existing federal law by providing relevant criminal history information to investigators.”

The social media checks have been controversial.

The Washington Times reported Monday that background check investigators are prohibited from looking at applicants’ social media accounts, in what analysts described as a major security loophole.

Several bills have been filed in Congress that would add social media checks to the background investigation process.

The Office of Personnel Management has said it questions the veracity of information found online, but the Obama administration says in its latest report that it will test social media as part of checks.

Rep. Elijah E. Cummings of Maryland, the ranking Democrat on the oversight committee, said he was happy to see recommendations like the one to push state and local law enforcement to cooperate with federal information requests.

But he said the government still relies too much on contractors to do much of the background investigation work.

“Judging the truthfulness of applicants in subject interviews and for top-secret clearances is an inherently governmental function with grave national security implications, and it must be federalized,” Mr. Cummings said.

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